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At least 991 records · Page 55Linked to original sources
PubMed2005

Correlation of AIB1 overexpression with advanced clinical stage of human colorectal carcinoma.

AIB1, a member of the steroid receptor coactivator 1 family, has been cloned on 20q12 and is a candidate oncogene in human breast cancer. It is commonly amplified and overexpressed in several types of human cancers. In this study, we examined the expression of AIB1, as related to clinicopathologic features, in 85 human colorectal cancers (CRCs). The status of the number of AIB1 copies, p53 expression, and DNA ploidy was also analyzed. The overexpression of AIB1 was detected in 35% of CRCs. Amplification of AIB1 was observed in 10% of CRCs. In addition, the overexpression of AIB1 was observed more frequently in CRCs in later clinical stages (T3 N1 M0/T3 N0 2M1), compared with that in T3 N0 M0 stage (P < .05). These results suggest that overexpression of AIB1 might provide a selective advantage for the developmental growth and/or progression of subsets of CRCs. In addition, a significant correlation (P < .05) of overexpression of AIB1 with p53 overexpression as well as with aneuploid DNA content was observed in these CRCs. The overexpression of p53 was also correlated significantly with CRC DNA ploidy (P < .05). Furthermore, there was a substantial population of CRCs showing overexpression of both AIB1 and p53 protein and all had aneuploid DNA content; most of these were in the later clinical stage. These findings suggest a possible convergence of AIB1 with a pathway involving p53, which might induce chromosomal instability and affect the clinical phenotype of a subset of CRCs.

Acetyltransferases↗
PubMed2006

Proteome chips for whole-organism assays.

Over the past 5 years, protein-chip technology has emerged as a useful tool for the study of many kinds of protein interactions and biochemical activities. The construction of Saccharomyces cerevisiae whole-proteome arrays has enabled further studies of such interactions in a proteome-wide context. Here, we explore some of the recent advances that have been made at the '-omic' level using protein microarrays.

Animals↗
PubMed2004

Sequential phases of cortical specification involve Neurogenin-dependent and -independent pathways.

Neocortical projection neurons, which segregate into six cortical layers according to their birthdate, have diverse morphologies, axonal projections and molecular profiles, yet they share a common cortical regional identity and glutamatergic neurotransmission phenotype. Here we demonstrate that distinct genetic programs operate at different stages of corticogenesis to specify the properties shared by all neocortical neurons. Ngn1 and Ngn2 are required to specify the cortical (regional), glutamatergic (neurotransmitter) and laminar (temporal) characters of early-born (lower-layer) neurons, while simultaneously repressing an alternative subcortical, GABAergic neuronal phenotype. Subsequently, later-born (upper-layer) cortical neurons are specified in an Ngn-independent manner, requiring instead the synergistic activities of Pax6 and Tlx, which also control a binary choice between cortical/glutamatergic and subcortical/GABAergic fates. Our study thus reveals an unanticipated heterogeneity in the genetic mechanisms specifying the identity of neocortical projection neurons.

Animals↗
PubMed2006

A rapid test for the diagnosis of thrombotic thrombocytopenic purpura using surface enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-mass spectrometry.

BACKGROUND: Thrombotic thrombocytopenic purpura (TTP), a life-threatening thrombotic microangiopathy, requires immediate diagnosis and plasma exchange therapy. Development of TTP is related to functional deficiency of ADAMTS-13 protease that leads to the accumulation of ultra large von Willebrand factor (VWF) and subsequent platelet thrombosis. Currently no clinical test is available for the rapid detection of ADAMTS-13 activity. OBJECTIVES: The goal is to devise a novel method to rapidly detect functional activity of ADAMTS-13 and improve clinical outcome. METHODS AND RESULTS: A recombinant VWF substrate containing the ADAMTS-13 cleavage site and a 6X Histidine tag was cleaved by ADAMTS-13 in a dose-dependent manner, generating approximately 7739 Da peptide containing a 6X Histidine tag. This cleaved peptide, bound to an IMAC/Nickel ProteinChip, was quantified using Surface Enhanced Laser Desorption/Ionization Time-of-flight Mass Spectrometry (SELDI-TOF-MS). The assay is capable of quantifying ADAMTS-13 activity as low as 2.5% in plasma within 4 h. When the cleaved peptide was quantified as a ratio of an internal control peptide, the test displayed good reproducibility, with an average inter-assay coefficient of variation (CV) of < 33%. Further validation revealed a mean ADAMTS-13 activity of 92.5% +/- 16.6% in 39 healthy donors. Sixteen patients with idiopathic TTP displayed mean ADAMTS-13 activity of 1.73% +/- 3.62%. Further utility of this novel method includes determining the inhibitory titer of ADAMTS-13 antibody in cases of acquired TTP. CONCLUSIONS: We have devised a novel SELDI-TOF-MS assay that offers a rapid, cost-effective, and functionally relevant test for timely diagnosis and management of TTP.

ADAM Proteins↗
PubMed2006

Human saliva proteome and transcriptome.

This paper tests the hypothesis that salivary proteins and their counterpart mRNAs co-exist in human whole saliva. Global profiling of human saliva proteomes and transcriptomes by mass spectrometry (MS) and expression microarray technologies, respectively, revealed many similarities between saliva proteins and mRNAs. Of the function-known proteins identified in saliva, from 61 to 70% were also found present as mRNA transcripts. For genes not detected at both protein and mRNA levels, we made further efforts to determine if the counterpart is present. Of 19 selected genes detected only at the protein level, the mRNAs of 13 (68%) genes were found in saliva by RT-PCR. In contrast, of many mRNAs detected only by microarrays, their protein products were found in saliva, as reported previously by other investigators. The saliva transcriptome may provide preliminary insights into the boundary of the saliva proteome.

Adult↗
PubMed2006

Serum proteomic fingerprints of adult patients with severe acute respiratory syndrome.

BACKGROUND: Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a new coronavirus strain, SARS-CoV. Specific proteomic patterns might be present in serum in response to the infection and could be useful for early detection of the disease. METHODS: Using surface-enhanced laser desorption/ionization (SELDI) ProteinChip technology, we profiled and compared serum proteins of 39 patients with early-stage SARS infection and 39 non-SARS patients who were suspected cases during the SARS outbreak period. Proteomic patterns associated with SARS were identified by bioinformatic and biostatistical analyses. Features of interest were then purified and identified by tandem mass spectrometry. RESULTS: Twenty proteomic features were significantly different between the 2 groups. Fifteen were increased in the SARS group, and 5 were decreased. Their concentrations were correlated with 2 or more clinical and/or biochemical variables. Two were correlated with the SARS-CoV viral load. Hierarchical clustering analysis showed that a majority of the SARS patients (95%) had similar serum proteomic profiles and identified 2 subgroups with poor prognosis. ROC curve analysis identified individual features as potential biomarkers for SARS diagnosis (areas under ROC curves, 0.733-0.995). ROC curve areas were largest for an N-terminal fragment of complement C3c alpha chain (m/z 28 119) and an internal fragment of fibrinogen alpha-E chain (m/z 5908). Immunoglobulin kappa light chain (m/z 24 505) positively correlated with viral load. CONCLUSIONS: Specific proteomic fingerprints in the sera of adult SARS patients could be used to identify SARS cases early during onset with high specificity and sensitivity.

Adult↗
PubMed2005

Immobilization of histidine-tagged recombinant proteins onto micropatterned surfaces for cell-based functional assays.

This letter describes a method for preparing protein microarrays that allow the functional analysis of proteins at a cellular level. This method involves the utilization of recombinant proteins genetically engineered to carry a fusion tag that has an affinity for metal ions. A micropatterned alkanethiol monolayer was used to prepare a microarray having multiple spots with immobilized metal ions. The fusion protein was chelated to the spots under physiological conditions. The feasibility of the method was demonstrated by culturing neural stem cells on the microarray that displayed oligohistidine-tagged epidermal growth factor.

Animals↗
PubMed2005

Multiplexed electrical detection of cancer markers with nanowire sensor arrays.

We describe highly sensitive, label-free, multiplexed electrical detection of cancer markers using silicon-nanowire field-effect devices in which distinct nanowires and surface receptors are incorporated into arrays. Protein markers were routinely detected at femtomolar concentrations with high selectivity, and simultaneous incorporation of control nanowires enabled discrimination against false positives. Nanowire arrays allowed highly selective and sensitive multiplexed detection of prostate specific antigen (PSA), PSA-alpha1-antichymotrypsin, carcinoembryonic antigen and mucin-1, including detection to at least 0.9 pg/ml in undiluted serum samples. In addition, nucleic acid receptors enabled real-time assays of the binding, activity and small-molecule inhibition of telomerase using unamplified extracts from as few as ten tumor cells. The capability for multiplexed real-time monitoring of protein markers and telomerase activity with high sensitivity and selectivity in clinically relevant samples opens up substantial possibilities for diagnosis and treatment of cancer and other complex diseases.

Biomarkers, Tumor↗
PubMed2004

Detection of serum uric acid using the optical polymeric enzyme biochip system.

An optical polymeric biochip system based on the complementary metal oxide semiconductor (CMOS) photo array sensor and polymeric enzyme biochip for rapidly quantitating uric acid in a one-step procedure was developed. The CMOS sensor was designed with N(+)/P-well structure and manufactured using a standard 0.5 microm CMOS process. The polymeric enzyme biochip was immobilized with uricase-peroxidase and used to fill the reacting medium with the sample. This study encompasses the cloning of the Bacillus subtilis uricase gene and expression in Escherichia coli, as well as the purification of uricase and measurement of its activity. The cloned uricase gene included an open reading frame of 1491 nucleotides that encodes a protein of approximately 55 kDa. The expression of the putative MBP-fusion protein involved approximately 98 kDa of the protein. The CMOS sensor response was stronger at a higher temperature range of 20-40 degrees C, with optimal pH at 8.5. The calibration curve of purified uric acid was linear in the concentration range from 2.5 to 12.5 mg/dL. The results obtained for serum uric acid correlated quite closely with those obtained using the Beckman Synchron method.

Biosensing Techniques↗
PubMed2006

Identification of novel peptide safety markers for exocrine pancreatic toxicity induced by cyanohydroxybutene.

Historically, serum amylase and lipase levels have been used to indicate pancreas injury; however, these enzyme levels are often not predictive of pathology. In an effort to discover novel biomarkers of pancreatic acinar cell injury, we analyzed serum and pancreas tissue from cyanohydroxybutene (CHB)-treated male IGS rats using proteomics methods. CHB produces an "edematous pancreatitis," characterized by depletion of zymogen granules, acinar cell apoptosis, and mild to moderate inflammation. Secondary necrosis occurs at higher doses. Rats were treated with 150 mg/kg of CHB and samples were collected at 4, 8, and 24 h. Analyses of serum tryptic digests by surface-enhanced laser desorption-ionization mass spectrometry revealed two novel peptide biomarkers (RA1609 and RT2864) that were predictive of pancreatic damage. Levels of RA1609 decreased, while levels of RT2864 increased by 8 h following CHB treatment. The changes in RA1609 and RT2864 were detected in media from CHB-treated primary rat acini, demonstrating that these peptides are either of pancreatic cell origin or are produced by proteases released from acinar cells. Sequencing revealed that RA1609 is a fragment of rat albumin (accession number P02770, residues 348-360) and RT2864 is a portion of either rat trypsin III (accession number P08426, residues 39-65) or bovine trypsin (accession number P00760, residues 35-61). These two peptides, and possibly other fragments of serum proteins that are digested by pancreatic proteases, may be useful as safety markers for exocrine pancreatic toxicity during drug development or as biomarkers for the diagnosis and/or grading of severity of pancreatic disease.

Acute Disease↗
PubMed2005

Identification of two molecular groups of seminomas by using expression and tissue microarrays.

Highly effective tailored clinical management of testicular germ cell tumors is based on the identification of two major histologic subtypes: seminomatous and nonseminomatous germ cell tumors. Expression array analysis of these two histologic subtypes using hierarchical clustering reveals two tumor groups, one composed solely of seminomas and the other containing embryonal carcinomas and seminomas. Supervised analysis between these groups identified 55 significantly dysregulated genes (false discovery rate = 2.3). The genes with the highest overexpression in the first group compared with the second included SLC43A1 (POV1), NET-7, IGF2, and JUP; down-regulated genes included GRB7, PFKP, and CDC6. In situ hybridization of SLC43A1 mRNA showed significantly increased signal intensity in the seminomas. At the protein level, expression of the immunohistochemical markers cytokeratins (pan-cytokeratin staining), placental-like alkaline phosphatase, anti-cytokeratin clone 5.2, CD30, anion exchanger 1/3, junction plakoglobulin (JUP), and POU domain, class 5, transcription factor 1 (octomer-binding transcription factor 3/4) was significantly different between seminomas and embryonal tumors. Hierarchical clustering based on a refined protein expression profile identified two groups, the first consisting solely of seminomas the other of seminomas and embryonal carcinomas. No histomorphologic differences were observed between the two seminoma groups such as the presence or absence of lymphocytes or extent of stromal elements. In summary, using independent methodologies and samples, we have identified two groups of seminomas. One group of seminomas has a molecular profile similar to embryonal carcinoma. The findings in the current study may help explain aberrant immunoprofiles seen with some seminomas.

Amino Acid Transport System y+L↗
PubMed2004

Using tree analysis pattern and SELDI-TOF-MS to discriminate transitional cell carcinoma of the bladder cancer from noncancer patients.

OBJECTIVE: To determine whether SELDI protein profiling of urine coupled with a tree analysis pattern could differentiate TCC from noncancer patients. METHODS: The ProteinChip Arrays were performed on a ProteinChip PBS II reader of the ProteinChip Biomarker System. The study was divided into two phases: a preliminary phase with construction of tree analysis pattern, and a testing phase with test urine samples. Generation of the tree analysis pattern was performed by a training data set consisting of 104 samples. The validity of the tree analysis pattern was then challenged with a test set of 68 samples. RESULTS: Average of 187 mass peaks was detected in the urine samples, and five of these peaks were used to construct the tree analysis pattern. The classification pattern correctly predicted 91.67-94.64% of the samples for both of the two groups in the training set, for an overall correct classification of about 93%. The pattern correctly predicted 72.0% (49 of 68) of the test samples, with 71.4% (25 of 35) of the TCC samples, 72.7% (24 of 33) of the noncancer samples. CONCLUSIONS: The high sensitivity and specificity obtained by the urine protein profiling approach demonstrate that SELDI-TOF-MS combined with a tree analysis pattern can both facilitate discriminate TCC bladder cancer with noncancer and provide an innovative clinical diagnostic platform improve the detection of TCC bladder cancer patients.

Adult↗
PubMed2005

Membrane array characterization of 80 chemokines, cytokines, and growth factors in open- and closed-eye tears: angiogenin and other defense system constituents.

PURPOSE: To adapt membrane-bound antibody array (MA) technology to characterize the distribution of a wide range of bioactive trace proteins in reflex (RTF) and open-eye (OTF) and closed-eye (CTF) tear samples. METHODS: Tears were collected by capillary tube and centrifuged. A commercially available standard MA and a custom array were modified to maximize the sensitivity of detection and the signal-to-noise ratio, to assay RTF and individually pooled CTF and OTF samples for 80 chemokines, growth factors, cytokines, and angiogenic modulators. The reliability of data was assessed by Western blot and other methods. RESULTS: Coupling an ultrasensitive chemiluminescence substrate system to an MA and optimizing conditions enhanced the sensitivity several hundredfold, allowing the detection of approximately 40 of the 79 probed proteins on the standard array, most of which were shown to be elevated in CTF. Identified entities include the known constituents epidermal growth factor (EGF), monocyte chemoattractant protein (MCP)-1, IL-8, tissue inhibitor of metalloproteinase (TIMP)-1 and -2, and numerous previously undetected tear components, such as angiogenin (ANG), growth factors, and the CXC and CC chemokines IFN-gamma inducible protein (IP)-10, growth-related oncogene (GRO), epithelial neutrophil-activating protein (ENA)-78, and macrophage inflammatory protein (MIP)-3alpha. Identification of other proteins was hindered by high background on the negative control array. Using a less complex custom array dramatically reduced background and allowed the visualization in CTF of proteins, such as VEGF, that were not detected with the standard array. CONCLUSIONS: MAs are powerful tools for differential screening of tears for large numbers of trace proteins. Analysis allowed the identification of previously undetected proteins that may participate in the host defense system as well as demonstrated the profound change in tear composition associated with prolonged eye closure in a manner reflective of physiological function.

Adult↗